Starfysh integration of all ccRCC samples

This vignette provides the code using Starfysh spot deconvolution on given signatures through integrative spatial deconvolution from multiple samples. The datasets here include 19 distinct TLS postivie ccRCC tumor samples from which 9 are responders to ICI treatment and 10 are non-responders.

#Import needed modules
import os
import numpy as np
import pandas as pd
import torch
import matplotlib.pyplot as plt
import matplotlib.font_manager
from matplotlib import rcParams

import seaborn as sns
sns.set_style('white')

font_list = []
fpaths = matplotlib.font_manager.findSystemFonts()
for i in fpaths:
    try:
        f = matplotlib.font_manager.get_font(i)
        font_list.append(f.family_name)
    except RuntimeError:
        pass

font_list = set(font_list)
plot_font = 'Helvetica' if 'Helvetica' in font_list else 'FreeSans'

rcParams['font.family'] = plot_font
rcParams.update({'font.size': 10})
rcParams.update({'figure.dpi': 300})
rcParams.update({'figure.figsize': (3,3)})
rcParams.update({'savefig.dpi': 500})

import warnings
warnings.filterwarnings('ignore')

#Load starfysh
from starfysh import (AA, utils, plot_utils, post_analysis)
from starfysh import starfysh as sf_model

Create sample meta info

meta_info = [['P_1','P_1','processed_data/P_1/'],#Already downloaded, #First one is the name of the folder containing the data
             ['P_2','P_2','processed_data/P_2/'], #
             ['P_3','P_3','processed_data/P_3/'],#Already downloaded
             ['P_4','P_4','processed_data/P_4/'],#Already downloaded
             ['P_5','P_5','processed_data/P_5/'],#Already downloaded
             ['P_6','P_6','processed_data/P_6/'],#Already downloaded
             ['P_7','P_7','processed_data/P_7/'],#Already downloaded
             ['P_8','P_8','processed_data/P_8/'], #Already downloaded
             ['P_9','P_9','processed_data/P_9/'], #
            ['P_10','P_10','processed_data/P_10/'],#Already downloaded, #First one is the name of the folder containing the data
             ['P_11','P_11','processed_data/P_11/'], #
             ['P_12','P_12','processed_data/P_12/'],#Already downloaded
             ['P_13','P_13','processed_data/P_13/'],#Already downloaded
             ['P_14','P_14','processed_data/P_14/'],#Already downloaded
             ['P_15','P_15','processed_data/P_15/'],#Already downloaded
             ['P_16','P_16','processed_data/P_16/'],#Already downloaded
             ['P_17','P_17','processed_data/P_17/'], #Already downloaded
             ['P_18','P_18','processed_data/P_18/'],
             ['P_19','P_19','processed_data/P_19/'],
            ]
#CID44971_TNBC
meta_info = pd.DataFrame(meta_info,columns=['sample','anonymized_id','visiumPath'])
# Specify data paths
data_path = 'processed_data/' # root data directory
output_path = 'Starfysh_results/'
sample_id2 = 'outs' #name of the folder containing the data
#data_path = '../ToyData/'
#output_path = '../ToyData/Results_integrated/'
sig_file_name = 'Starfysh_results/Signatures_Starfysh.csv' #This is the Supplementary Table S13
print(meta_info)
for sample_id in meta_info['sample']:
    print(sample_id)
    data_path2 = meta_info['visiumPath'][list(meta_info['sample']).index(sample_id)]
    print(data_path2)

adata_all = []
adata_normed_all = []
img_metadata_all = {}
for sample_id in meta_info['sample']:
    print(sample_id)
    data_path2 = meta_info['visiumPath'][list(meta_info['sample']).index(sample_id)]
    adata, adata_normed = utils.load_adata(data_folder=data_path2,  # root data directory
                                       sample_id=sample_id2,  # sample_id
                                       n_genes=2000  # number of highly variable genes to keep
                                      )
    
    
    adata_all.append(adata)
    adata_normed_all.append(adata_normed)
    
    img_metadata = utils.preprocess_img(data_path2,
                                    sample_id2,
                                    adata_index=adata.obs.index,
                                    hchannel=True #Must be true otherwise POE wont work
                                    )
    #From: https://github.com/azizilab/starfysh/issues/31
    
    adata.obs['anonymized_id']=meta_info['anonymized_id'][list(meta_info['sample']).index(sample_id)]
    #adata.obs['RECIST_R_nR']=meta_info['RECIST_R_nR'][list(meta_info['sample']).index(sample_id)] #Clinical data can be
    #demanded to authors
    adata.obs['patient']=meta_info['sample'][list(meta_info['sample']).index(sample_id)]
    adata.obs['sample']=meta_info['sample'][list(meta_info['sample']).index(sample_id)]
    #sample_id_3 = meta_info['anonymized_id'][list(meta_info['sample']).index(sample_id)]
    adata.obs_names  = adata.obs_names+'-'+sample_id

    adata_normed.obs['anonymized_id']=adata.obs['anonymized_id']
    adata_normed.obs['patient']=adata.obs['patient']
    #adata_normed.obs['RECIST_R_nR']=adata.obs['RECIST_R_nR'] #Clinical data can be
    #demanded to authors

    img_metadata['map_info'].index = img_metadata['map_info'].index+'-'+sample_id
    img_metadata_all[sample_id] = img_metadata 

# Save concat data
import anndata
import scanpy as sc
adata_all = anndata.concat(adata_all)
adata_normed_all = anndata.concat(adata_normed_all)
sc.pp.highly_variable_genes(adata_normed_all)
adata_all.uns = adata_normed_all.uns
adata_all.var = adata_normed_all.var

#Check
print(adata_all)
print(adata_normed_all)

AnnData object with n_obs × n_vars = 75259 × 13200
    obs: 'in_tissue', 'array_row', 'array_col', 'sample', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_50_genes', 'pct_counts_in_top_100_genes', 'pct_counts_in_top_200_genes', 'pct_counts_in_top_500_genes', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'anonymized_id', 'RECIST_R_nR', 'patient'
    var: 'highly_variable', 'means', 'dispersions', 'dispersions_norm'
    uns: 'hvg'
    obsm: 'spatial'
AnnData object with n_obs × n_vars = 75259 × 13200
    obs: 'in_tissue', 'array_row', 'array_col', 'sample', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_50_genes', 'pct_counts_in_top_100_genes', 'pct_counts_in_top_200_genes', 'pct_counts_in_top_500_genes', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'anonymized_id', 'RECIST_R_nR', 'patient'
    var: 'highly_variable', 'means', 'dispersions', 'dispersions_norm'
    uns: 'hvg'
    obsm: 'spatial'

# Load signatures
gene_sig = pd.read_csv(os.path.join(sig_file_name))
gene_sig = utils.filter_gene_sig(gene_sig, adata_all.to_df())
gene_sig.head()

	Tcm	Tem	Tfh	Treg	Activated CD8	Dysfunc CD8	Terminal exhaustion	Precursor exhaustion	NK	B cells memory	...	Monocytes	cDC	pDC	CAFs MSC iCAF-like	CAFs myCAF-like	Endothelial	PT_like	ProInflammatory	EMT_like	PI3K
0	CCR7	IL7R	CXCL13	TNFRSF4	CD69	NPEPPS	CD3G	TCF7	GNLY	MS4A1	...	LYZ	CD80	IL3RA	APOD	COL1A1	ACKR1	TRPM3	AL078604.4	EEF1G	ERBB4
1	LTB	ANXA1	NMB	LTB	CCR7	NOTCH2	FASLG	MS4A4A	XCL1	CD79A	...	IL1B	CD86	LILRA4	DCN	COL1A2	FABP4	PBX1	BIRC3	FAU	GRHL2
2	IL7R	CXCR4	NR3C1	IL32	CD27	CABLES1	ID2	TNFSF8	XCL2	CD83	...	G0S2	CCR7	CD123	PTGDS	COL3A1	PLVAP	SLC6A13	DCLK1	UBA52	SIM2
3	SARAF	KLRB1	DUSP4	BATF	BTLA	CERK	LAG3	CXCL10	AREG	CD37	...	TYROBP	CD1A	TCF4	CFD	LUM	RAMP2	SLC17A4	PDE10A	MIF	SCHLAP1
4	SELL	TNFAIP3	TNFRSF18	FOXP3	CD40LG	MTMR3	RGS1	EEF1B2	KLRD1	BANK1	...	FCN1	CD1C	IRF7	LUM	SFRP2	VWF	SLC6A12	FKBP5	EEF2	ESRP1

5 rows × 25 columns

#Save data
# Save concat data
import anndata
import scanpy as sc
#adata_all.write(os.path.join(output_path, 'adata_all.h5ad'))
#adata_normed_all.write(os.path.join(output_path, 'adata_normed_all.h5ad'))

... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical
... storing 'patient' as categorical
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical
... storing 'patient' as categorical

#Load if needed
# Save concat data
import anndata
import scanpy as sc
adata_all = sc.read_h5ad(os.path.join(output_path, 'adata_all.h5ad'))
adata_normed_all = sc.read_h5ad(os.path.join(output_path, 'adata_normed_all.h5ad'))

Preprocessing: Run archetypes separately to update gene signature

from starfysh.AA import ArchetypalAnalysis
def assign_archetypes(anchor_df, r=30):
    """
    Assign best 1-1 mapping of archetype community to its closest anchor community (cell-type specific anchor spots)
    Criteria: choose the top cell type in which its anchors belongs to the top r neighbors to the given archetype

    Parameters
    ----------
    anchor_df : pd.DataFrame
        Dataframe of anchor spot indices

`       r : int
        Resolution parameter to threshold archetype - anchor mapping

    Returns
    -------
    map_df : pd.DataFrame
        DataFrame of overlapping spot ratio of each anchor `i` to archetype `j`

    map_dict : dict
        Dictionary of cell type -> mapped archetype
    """
    assert aa_model.arche_df is not None, "Please compute archetypes & assign nearest-neighbors first!"

    n_nbrs, n_archetypes = aa_model.arche_df.shape # number of archetypal spots for each archtype, number of archetypes
    x_concat = np.vstack([aa_model.count, aa_model.archetype])
    anchor_nbrs = anchor_df.values
    archetypal_nbrs = aa_model._get_knns(x_concat, n_nbrs=r, indices=aa_model.n_spots+aa_model.major_idx).T  # r-nearest nbrs to each archetype

    
    
    print(archetypal_nbrs.shape)
    overlaps = np.array(
        [
            [
                len(np.intersect1d(anchor_nbrs[:, i], archetypal_nbrs[:, j]))
                for j in range(archetypal_nbrs.shape[1])
            ]
            for i in range(anchor_nbrs.shape[1])
        ]
    )
    overlaps_df = pd.DataFrame(overlaps, index=anchor_df.columns, columns=aa_model.arche_df.columns)
    arche_argmaxs = overlaps.argmax(0)
    
    distance_df = pd.DataFrame(np.zeros([anchor_df.shape[1],
                                         aa_model.arche_df.shape[1]]), 
                               index=anchor_df.columns, 
                               columns=aa_model.arche_df.columns
                              )
    for i in range(distance_df.shape[0]):
        for j in range(distance_df.shape[1]):
            dist_tmp = 0
            for kk in anchor_df.iloc[:,i]:
                dist_tmp += np.linalg.norm(aa_model.count[kk,:] - 
                                           aa_model.archetype[j,:]
                                          )
            
            distance_df.iloc[i,j] = dist_tmp
    
    map_dict = {}
    for k in range(overlaps.shape[0]):
        list_ = np.argsort(overlaps[k])[::-1]
        for i in list_:
            if (np.argsort(overlaps[:,i])[::-1][0]==k):
                if ((overlaps[k,:]==overlaps[k,i]).sum()==1):
                    map_dict[anchor_df.columns[k]]=aa_model.arche_df.columns[i]
                break 
                
                
    map_dict2 = {}
    for k in range(distance_df.shape[0]):
        list_ = np.argsort(np.array(distance_df)[k])
        #print(list_)
        for i in list_:
            if (np.argsort(np.array(distance_df)[:,i])[0]==k):
                if ((np.array(distance_df)[k,:]==np.array(distance_df)[k,i]).sum()==1):
                    map_dict2[anchor_df.columns[k]]=aa_model.arche_df.columns[i]
                break 
                
    return overlaps_df, distance_df,map_dict,map_dict2

import importlib
importlib.reload(utils)

gene_sig_all = []
visium_args_all = {}
for sample_id in meta_info['anonymized_id']:
    print(sample_id)
    adata = adata_all[adata_all.obs['anonymized_id']==sample_id]
    adata_normed = adata_normed_all[adata_normed_all.obs['anonymized_id']==sample_id]
    
    sc.pp.highly_variable_genes(adata_normed)
    adata.uns = adata_normed.uns
    adata.var = adata_normed.var

    img_metadata = img_metadata_all[sample_id]
    
    visium_args = utils.VisiumArguments(adata,
                                    adata_normed,
                                    gene_sig,
                                    img_metadata,
                                    window_size=4,
                                    sample_id=sample_id2,#'outs'
                                    n_img_chan = 1,
                                   )
    adata, adata_normed = visium_args.get_adata()
    anchors_df = visium_args.get_anchors()
    aa_model = AA.ArchetypalAnalysis(adata_orig=adata,
                                      # n_neighbors=100  #Atgument not detected
                                    )
    archetype, arche_dict, major_idx, evs = aa_model.compute_archetypes(cn=100, 
                                                                    #r=5,  not used
                                                                    converge=1e-3,
                                                                    display=False)

    arche_df = aa_model.find_archetypal_spots()
    
    markers_df = aa_model.find_markers(n_markers=30, display=False)
    
    percent_anchor = 0.01
    map_df, distance_df,map_dict,map_dict2 = assign_archetypes(anchors_df[:int(percent_anchor*adata.shape[0])], 
                                     r=int(percent_anchor*adata.shape[0])
                                    )  # here we subset the `r` top archetypes
    gene_sig_arch = gene_sig.copy()

    for cell_type in map_dict.keys():
        arch = map_dict[cell_type]
        gene_sig_arch = utils.append_sigs(gene_sig_arch, cell_type, markers_df[arch], n_genes=10)
    gene_sig_all.append(gene_sig_arch)
    visium_args_all[sample_id] = visium_args

P_1

[2024-04-29 11:05:47] Subsetting highly variable & signature genes ...
[2024-04-29 11:05:55] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 11:05:55] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 11:05:57] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 11:06:00] Computing intrinsic dimension to estimate k...

23 components are retained using conditional_number=100.00

[2024-04-29 11:06:01] Estimating lower bound of # archetype as 8...
[2024-04-29 11:07:14] 0.8892 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 11:07:14] Finding 100 nearest neighbors for each archetype...
[2024-04-29 11:07:14] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(13, 14)
P_2

[2024-04-29 11:07:19] Subsetting highly variable & signature genes ...
[2024-04-29 11:08:06] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 11:08:09] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 11:08:14] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 11:08:47] Computing intrinsic dimension to estimate k...

30 components are retained using conditional_number=100.00

[2024-04-29 11:08:48] Estimating lower bound of # archetype as 11...
[2024-04-29 11:11:13] 0.8618 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 11:11:13] Finding 100 nearest neighbors for each archetype...
[2024-04-29 11:11:13] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(47, 16)
P_3

[2024-04-29 11:11:27] Subsetting highly variable & signature genes ...
[2024-04-29 11:11:59] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 11:12:00] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 11:12:04] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 11:12:27] Computing intrinsic dimension to estimate k...

27 components are retained using conditional_number=100.00

[2024-04-29 11:12:28] Estimating lower bound of # archetype as 12...
[2024-04-29 11:14:35] 0.8875 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 11:14:35] Finding 100 nearest neighbors for each archetype...
[2024-04-29 11:14:35] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(38, 16)
P_4

[2024-04-29 11:14:48] Subsetting highly variable & signature genes ...
[2024-04-29 11:14:56] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 11:14:57] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 11:14:59] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 11:15:06] Computing intrinsic dimension to estimate k...
[2024-04-29 11:15:06] Estimating lower bound of # archetype as 12...

30 components are retained using conditional_number=100.00

[2024-04-29 11:17:58] 0.8667 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 11:17:58] Finding 100 nearest neighbors for each archetype...
[2024-04-29 11:17:58] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(20, 18)
P_5

[2024-04-29 11:18:05] Subsetting highly variable & signature genes ...
[2024-04-29 11:18:58] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 11:19:00] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 11:19:05] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 11:19:42] Computing intrinsic dimension to estimate k...

30 components are retained using conditional_number=100.00

[2024-04-29 11:19:43] Estimating lower bound of # archetype as 11...
[2024-04-29 11:26:03] 0.8954 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 11:26:03] Finding 100 nearest neighbors for each archetype...
[2024-04-29 11:26:03] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(49, 20)
P_6

[2024-04-29 11:26:30] Subsetting highly variable & signature genes ...
[2024-04-29 11:26:58] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 11:27:01] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 11:27:06] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 11:27:42] Computing intrinsic dimension to estimate k...

30 components are retained using conditional_number=100.00

[2024-04-29 11:27:43] Estimating lower bound of # archetype as 12...
[2024-04-29 11:42:19] 0.7654 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 11:42:19] Finding 100 nearest neighbors for each archetype...
[2024-04-29 11:42:20] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(49, 20)
P_7

[2024-04-29 11:43:06] Subsetting highly variable & signature genes ...
[2024-04-29 11:44:37] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 11:44:38] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 11:44:41] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 11:44:52] Computing intrinsic dimension to estimate k...

30 components are retained using conditional_number=100.00

[2024-04-29 11:44:52] Estimating lower bound of # archetype as 16...
[2024-04-29 11:48:29] 0.7851 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 11:48:29] Finding 100 nearest neighbors for each archetype...
[2024-04-29 11:48:29] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(25, 20)
P_8

[2024-04-29 11:48:38] Subsetting highly variable & signature genes ...
[2024-04-29 11:48:59] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 11:49:00] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 11:49:03] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 11:49:19] Computing intrinsic dimension to estimate k...

29 components are retained using conditional_number=100.00

[2024-04-29 11:49:20] Estimating lower bound of # archetype as 10...
[2024-04-29 11:52:33] 0.8909 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 11:52:33] Finding 100 nearest neighbors for each archetype...
[2024-04-29 11:52:33] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(32, 16)
P_9

[2024-04-29 11:52:43] Subsetting highly variable & signature genes ...
[2024-04-29 11:52:50] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 11:52:50] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 11:52:52] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 11:52:54] Computing intrinsic dimension to estimate k...
[2024-04-29 11:52:55] Estimating lower bound of # archetype as 12...

30 components are retained using conditional_number=100.00

[2024-04-29 11:54:00] 0.8711 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 11:54:00] Finding 100 nearest neighbors for each archetype...
[2024-04-29 11:54:00] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(10, 13)
P_10

[2024-04-29 11:54:04] Subsetting highly variable & signature genes ...
[2024-04-29 11:54:33] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 11:54:35] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 11:54:40] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 11:55:14] Computing intrinsic dimension to estimate k...

30 components are retained using conditional_number=100.00

[2024-04-29 11:55:15] Estimating lower bound of # archetype as 8...
[2024-04-29 12:00:41] 0.9363 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 12:00:41] Finding 100 nearest neighbors for each archetype...
[2024-04-29 12:00:41] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(47, 21)
P_11

[2024-04-29 12:01:05] Subsetting highly variable & signature genes ...
[2024-04-29 12:02:07] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 12:02:09] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 12:02:14] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 12:02:52] Computing intrinsic dimension to estimate k...

30 components are retained using conditional_number=100.00

[2024-04-29 12:02:52] Estimating lower bound of # archetype as 11...
[2024-04-29 12:09:08] 0.9184 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 12:09:08] Finding 100 nearest neighbors for each archetype...
[2024-04-29 12:09:09] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(49, 27)
P_12

[2024-04-29 12:09:39] Subsetting highly variable & signature genes ...
[2024-04-29 12:10:08] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 12:10:10] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 12:10:15] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 12:10:48] Computing intrinsic dimension to estimate k...

30 components are retained using conditional_number=100.00

[2024-04-29 12:10:49] Estimating lower bound of # archetype as 13...
[2024-04-29 12:11:49] 0.8439 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 12:11:49] Finding 100 nearest neighbors for each archetype...
[2024-04-29 12:11:49] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(47, 14)
P_13

[2024-04-29 12:11:58] Subsetting highly variable & signature genes ...
[2024-04-29 12:12:27] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 12:12:29] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 12:12:34] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 12:13:05] Computing intrinsic dimension to estimate k...

30 components are retained using conditional_number=100.00

[2024-04-29 12:13:06] Estimating lower bound of # archetype as 8...
[2024-04-29 12:18:12] 0.9134 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 12:18:12] Finding 100 nearest neighbors for each archetype...
[2024-04-29 12:18:13] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(45, 26)
P_14

[2024-04-29 12:18:29] Subsetting highly variable & signature genes ...
[2024-04-29 12:18:51] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 12:18:53] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 12:18:57] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 12:19:17] Computing intrinsic dimension to estimate k...

30 components are retained using conditional_number=100.00

[2024-04-29 12:19:17] Estimating lower bound of # archetype as 7...
[2024-04-29 12:23:24] 0.9085 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 12:23:24] Finding 100 nearest neighbors for each archetype...
[2024-04-29 12:23:24] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(35, 23)
P_15

[2024-04-29 12:23:44] Subsetting highly variable & signature genes ...
[2024-04-29 12:24:28] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 12:24:30] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 12:24:35] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 12:25:12] Computing intrinsic dimension to estimate k...

30 components are retained using conditional_number=100.00

[2024-04-29 12:25:13] Estimating lower bound of # archetype as 8...
[2024-04-29 12:30:53] 0.8859 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 12:30:53] Finding 100 nearest neighbors for each archetype...
[2024-04-29 12:30:54] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(49, 25)
P_16

[2024-04-29 12:31:27] Subsetting highly variable & signature genes ...
[2024-04-29 12:31:45] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 12:31:47] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 12:31:52] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 12:32:24] Computing intrinsic dimension to estimate k...

30 components are retained using conditional_number=100.00

[2024-04-29 12:32:24] Estimating lower bound of # archetype as 7...
[2024-04-29 12:37:15] 0.84 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 12:37:15] Finding 100 nearest neighbors for each archetype...
[2024-04-29 12:37:16] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(46, 25)
P_17

[2024-04-29 12:37:35] Subsetting highly variable & signature genes ...
[2024-04-29 12:38:03] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 12:38:05] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 12:38:10] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 12:38:47] Computing intrinsic dimension to estimate k...

30 components are retained using conditional_number=100.00

[2024-04-29 12:38:48] Estimating lower bound of # archetype as 11...
[2024-04-29 12:44:57] 0.9504 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 12:44:58] Finding 100 nearest neighbors for each archetype...
[2024-04-29 12:44:58] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(49, 24)
P_18

[2024-04-29 12:45:26] Subsetting highly variable & signature genes ...
[2024-04-29 12:45:58] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 12:46:00] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 12:46:05] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 12:46:33] Computing intrinsic dimension to estimate k...

30 components are retained using conditional_number=100.00

[2024-04-29 12:46:34] Estimating lower bound of # archetype as 10...
[2024-04-29 12:52:06] 0.9056 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 12:52:06] Finding 100 nearest neighbors for each archetype...
[2024-04-29 12:52:06] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(43, 21)
P_19

[2024-04-29 12:52:23] Subsetting highly variable & signature genes ...
[2024-04-29 12:52:57] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 12:52:59] Retrieving & normalizing signature gene expressions...

WARNING: genes are not in var_names and ignored: ['SARAF', 'BTG1']
WARNING: genes are not in var_names and ignored: ['FYB', 'IL21']
WARNING: genes are not in var_names and ignored: ['AC133644.2', 'CACYBP', 'LAIR2', 'BTG1']
WARNING: genes are not in var_names and ignored: ['IFNG', 'CD95L']
WARNING: genes are not in var_names and ignored: ['KLF3', 'MIR466I', 'TUBB2B', 'MNDAL', 'TMEM55B', 'FAM196B']
WARNING: genes are not in var_names and ignored: ['CCL3 CCL3L1', 'CD160', 'PLAC8', 'ARL6IP1']
WARNING: genes are not in var_names and ignored: ['XCL2', 'KRT86']
WARNING: genes are not in var_names and ignored: ['CD83', 'HLA-DQB1', 'HLA-DQA2', 'LINC00926', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['TCL1A', 'LINC00926', 'HLA-DQB1', 'FCER2', 'CD83', 'BACH2', 'BTG1', 'FAM129C', 'HLA-DQA2', 'HLA-DRB5']
WARNING: genes are not in var_names and ignored: ['CCL3', 'CCL3L3', 'SEPP1', 'HLA-DRB1', 'GPX1', 'HLA-DRB5', 'HLA-DQB1', 'CD83', 'CCL4L2']
WARNING: genes are not in var_names and ignored: ['FAM26F', 'HLA-DRB5', 'HLA-DRB1', 'CCL3', 'HLA-DQB1', 'CCL3L3', 'GPX1']
WARNING: genes are not in var_names and ignored: ['IGKV3-15', 'IGKV1-5', 'IGKV3-20', 'IGKV3-11', 'IGKV1-9', 'IGLV2-14', 'IGLV3-25', 'IGLV1-40', 'IGLV1-44', 'IGHV6-1', 'IGLC2', 'IGLV1-51', 'IGHV3-23', 'IGHV3-21', 'IGLV3-21', 'IGLC3', 'IGLV1-47', 'IGHV3-30', 'IGLV3-1', 'IGLV2-23', 'IGLV2-11', 'IGHV4-39', 'IGHV1-18', 'IGHV1-46', 'CH17-224D4.2', 'IGLV2-8', 'IGKV1-8', 'IGLV4-69', 'IGKV1-16', 'IGKV3D-11', 'IGHV3-15', 'IGHV3-74', 'IGLV3-19']
WARNING: genes are not in var_names and ignored: ['ARG1']
WARNING: genes are not in var_names and ignored: ['GPX1', 'HLA-DRB1', 'HLA-DRB5', 'HLA-DQB1', 'FAM26F', 'RP11-1143G9.4', 'CCL3', 'CCL3L3', 'CD83']
WARNING: genes are not in var_names and ignored: ['CD1A', 'CD1C', 'CD11b', 'CD11C', 'CD16', 'CD83', 'CD123', 'CD141', 'EpCAM', 'HLA-DR', 'CD207', 'CD172A']
WARNING: genes are not in var_names and ignored: ['CD123', 'IFNA', 'IFNB', 'TNFA']
WARNING: genes are not in var_names and ignored: ['IGF2', 'CYR61', 'CTGF', 'MEG3']
WARNING: genes are not in var_names and ignored: ['CTGF']
WARNING: genes are not in var_names and ignored: ['SDPR', 'PDLIM1', 'PTRF', 'FLT1', 'CXorf36']
WARNING: genes are not in var_names and ignored: ['TRPM3', 'SLC17A4', 'CCSER1', 'SLC6A3', 'AC124854.1', 'ACSM2B', 'SLC5A8', 'FTCD', 'SLC27A2', 'PCK1', 'CDHR2', 'ACE2', 'HAVCR1', 'ZMAT4', 'ACMSD', 'UGT2A3']
WARNING: genes are not in var_names and ignored: ['AL078604.4', 'AP002518.2', 'MIR31HG']
WARNING: genes are not in var_names and ignored: ['FAU', 'TMSB10', 'GAPDH', 'TPT1', 'TUBB']
WARNING: genes are not in var_names and ignored: ['ERBB4', 'GRHL2', 'SIM2', 'SCHLAP1', 'ESRP1', 'TMPRSS4', 'GABRP', 'ADGRF1', 'SLC12A1', 'LYPD6B', 'ARHGEF38', 'LRP1B', 'PRDM16', 'PWRN1', 'HS6ST3']

[2024-04-29 12:53:05] Identifying anchor spots (highly expression of specific cell-type signatures)...
[2024-04-29 12:53:41] Computing intrinsic dimension to estimate k...

30 components are retained using conditional_number=100.00

[2024-04-29 12:53:42] Estimating lower bound of # archetype as 10...
[2024-04-29 12:59:37] 0.934 variance explained by raw archetypes.
Merging raw archetypes within 100 NNs to get major archetypes
[2024-04-29 12:59:37] Finding 100 nearest neighbors for each archetype...
[2024-04-29 12:59:38] Finding 30 top marker genes for each archetype...
... storing 'sample' as categorical
... storing 'anonymized_id' as categorical
... storing 'RECIST_R_nR' as categorical

(49, 23)

gene_sig

	Tcm	Tem	Tfh	Treg	Activated CD8	Dysfunc CD8	Terminal exhaustion	Precursor exhaustion	NK	B cells memory	...	Monocytes	cDC	pDC	CAFs MSC iCAF-like	CAFs myCAF-like	Endothelial	PT_like	ProInflammatory	EMT_like	PI3K
0	CCR7	IL7R	CXCL13	TNFRSF4	CD69	NPEPPS	CD3G	TCF7	GNLY	MS4A1	...	LYZ	CD80	IL3RA	APOD	COL1A1	ACKR1	TRPM3	AL078604.4	EEF1G	ERBB4
1	LTB	ANXA1	NMB	LTB	CCR7	NOTCH2	FASLG	MS4A4A	XCL1	CD79A	...	IL1B	CD86	LILRA4	DCN	COL1A2	FABP4	PBX1	BIRC3	FAU	GRHL2
2	IL7R	CXCR4	NR3C1	IL32	CD27	CABLES1	ID2	TNFSF8	XCL2	CD83	...	G0S2	CCR7	CD123	PTGDS	COL3A1	PLVAP	SLC6A13	DCLK1	UBA52	SIM2
3	SARAF	KLRB1	DUSP4	BATF	BTLA	CERK	LAG3	CXCL10	AREG	CD37	...	TYROBP	CD1A	TCF4	CFD	LUM	RAMP2	SLC17A4	PDE10A	MIF	SCHLAP1
4	SELL	TNFAIP3	TNFRSF18	FOXP3	CD40LG	MTMR3	RGS1	EEF1B2	KLRD1	BANK1	...	FCN1	CD1C	IRF7	LUM	SFRP2	VWF	SLC6A12	FKBP5	EEF2	ESRP1
...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...	...
95	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
96	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
97	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
98	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN
99	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	...	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN	NaN

100 rows × 25 columns

Preprocessing: integrate data

This step is for identifying the anchor spots and providing prior for model training.

utils.VisiumArguments is called for each sample (performed already when updating the signature using archetypes, stored as 'visium_args_all'), followed by utils_integrate.VisiumArguments_integrate for integrating all priors.

Starfysh calcualates cell-type proportion scores for each spot per sample given the annotated signatures (per cell type) as the model's prior

Each spot will be ranked (anchors_df) based on the prior, which represents the rough estimation of the given cell-type's enrichment

adata_normed_all

AnnData object with n_obs × n_vars = 75259 × 13200
    obs: 'in_tissue', 'array_row', 'array_col', 'sample', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_50_genes', 'pct_counts_in_top_100_genes', 'pct_counts_in_top_200_genes', 'pct_counts_in_top_500_genes', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'anonymized_id', 'RECIST_R_nR', 'patient'
    var: 'highly_variable', 'means', 'dispersions', 'dispersions_norm'
    uns: 'hvg'
    obsm: 'spatial'

from starfysh import utils_integrate
importlib.reload(utils_integrate)

sc.pp.highly_variable_genes(adata_normed_all)
adata_all.uns = adata_normed_all.uns
adata_all.var = adata_normed_all.var


visium_args = utils_integrate.VisiumArguments_integrate(adata_all,
                                    adata_normed_all,
                                    gene_sig, ##Stay with normal signature
                                    img_metadata_all,
                                    visium_args_all,                                        
                                    window_size=3,
                                    sample_id=meta_info['sample']
                                   )

[2024-04-29 19:40:18] Subsetting highly variable & signature genes ...
[2024-04-29 19:40:21] Smoothing library size by taking averaging with neighbor spots...
[2024-04-29 19:40:58] Retrieving & normalizing signature gene expressions...
[2024-04-29 19:40:58] Identifying anchor spots (highly expression of specific cell-type signatures)...

import importlib
importlib.reload(sf_model)

from starfysh import utils_integrate
importlib.reload(utils_integrate)

<module 'starfysh.utils_integrate' from '/home/isaias/.local/share/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/starfysh/utils_integrate.py'>

Processing: Run Starfysh for joint spatial deconvolution & sample integration

(1) Model parameters

n_repeats = 1
epochs = 100
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')

import importlib
importlib.reload(utils_integrate)

<module 'starfysh.utils_integrate' from '/home/isaias/.local/share/r-miniconda/envs/r-reticulate/lib/python3.8/site-packages/starfysh/utils_integrate.py'>

adata

AnnData object with n_obs × n_vars = 4936 × 13200
    obs: 'in_tissue', 'array_row', 'array_col', 'sample', 'n_genes_by_counts', 'log1p_n_genes_by_counts', 'total_counts', 'log1p_total_counts', 'pct_counts_in_top_50_genes', 'pct_counts_in_top_100_genes', 'pct_counts_in_top_200_genes', 'pct_counts_in_top_500_genes', 'total_counts_mt', 'log1p_total_counts_mt', 'pct_counts_mt', 'anonymized_id', 'RECIST_R_nR', 'patient'
    var: 'highly_variable', 'means', 'dispersions', 'dispersions_norm'
    uns: 'hvg', 'cell_types'
    obsm: 'spatial'

(2). Model training

model, loss = utils_integrate.run_starfysh(visium_args,
                                 n_repeats=n_repeats,
                                 epochs=epochs,
                                 poe=True, #Means histology to be used...
                                 device=device)

[2024-04-29 20:00:28] Running Starfysh with 1 restarts, choose the model with best parameters...
[2024-04-29 20:00:28]  ===  Restart Starfysh 1 === 

[2024-04-29 20:00:28] Initializing model parameters...
[2024-04-29 20:14:26] Epoch[10/100], train_loss: 7163.9827, train_reconst: 6954.7536, train_u: 13.5052,train_z: 36.2660,train_c: 95.8831,train_n: 63.5748
[2024-04-29 20:28:17] Epoch[20/100], train_loss: 6653.4592, train_reconst: 6451.1382, train_u: 12.1844,train_z: 41.8874,train_c: 83.4769,train_n: 64.7722
[2024-04-29 20:42:08] Epoch[30/100], train_loss: 6666.6284, train_reconst: 6469.7888, train_u: 11.8632,train_z: 41.5447,train_c: 78.2523,train_n: 65.1794
[2024-04-29 20:55:50] Epoch[40/100], train_loss: 6518.8326, train_reconst: 6326.1833, train_u: 11.8387,train_z: 40.8535,train_c: 74.3282,train_n: 65.6289
[2024-04-29 21:09:40] Epoch[50/100], train_loss: 6423.5089, train_reconst: 6233.7970, train_u: 11.9583,train_z: 40.5227,train_c: 71.1362,train_n: 66.0947
[2024-04-29 21:23:35] Epoch[60/100], train_loss: 6381.2035, train_reconst: 6193.9551, train_u: 12.1276,train_z: 40.1263,train_c: 68.3863,train_n: 66.6083
[2024-04-29 21:37:49] Epoch[70/100], train_loss: 6342.5779, train_reconst: 6157.7389, train_u: 12.2960,train_z: 39.6013,train_c: 66.2523,train_n: 66.6894
[2024-04-29 21:52:11] Epoch[80/100], train_loss: 6252.4254, train_reconst: 6069.1305, train_u: 12.4573,train_z: 39.4165,train_c: 64.4898,train_n: 66.9313
[2024-04-29 22:06:36] Epoch[90/100], train_loss: 6224.7530, train_reconst: 6043.2759, train_u: 12.5965,train_z: 38.7373,train_c: 63.0056,train_n: 67.1377
[2024-04-29 22:21:00] Epoch[100/100], train_loss: 6199.6327, train_reconst: 6019.8916, train_u: 12.7062,train_z: 38.0655,train_c: 61.8222,train_n: 67.1472
[2024-04-29 22:21:00] Saving the best-performance model...
[2024-04-29 22:21:00]  === Finished training === 

# Save model
torch.save(model.state_dict(), os.path.join(output_path, 'integ_model.pt'))

inference_outputs, generative_outputs = sf_model.model_eval_integrate(model,
                                                                      visium_args.adata,
                                                                      visium_args,
                                                                      poe=True,
                                                                      device=device
                                                                     )

rv: px_r_poe can't be stored

##Extract integrated object to a different object
adata_integrate = visium_args.adata.copy()
adata_integrate.shape

(75259, 2738)

adata_inte_2 = adata_integrate.copy() #Copy just in case

#save integrated object
adata_inte_2.write(os.path.join(output_path,'adata_integrated.h5ad'))

##
# Deconvolution prediction
prop_pred_df = pd.DataFrame(adata_integrate.obsm['qc_m'], index=adata_integrate.obs_names, columns=gene_sig.columns)
prop_pred_df

##Save deconvolution values
##Export results from deconvolution...
prop_pred_df.to_csv(os.path.join(output_path,'Starfysh_integrated_obs_all.csv'), index=True) ##This file is needed
#to reproduce Figure 3 and 4

###UMAP before sample integration
adata_all2 = adata_all[:, adata_integrate.var_names]
sc.pp.neighbors(adata_all2, use_rep='X', n_neighbors=20)
sc.tl.umap(adata_all2, min_dist=0.2)

#Plot
fig, ax = plt.subplots(1, 1, figsize=(10, 10), dpi=200)
ax = sc.pl.umap(adata_all2, color='anonymized_id', 
               frameon=False, s=25, ax=ax,
               title='UMAP without Starfysh sample integration'
              )
fig.savefig(os.path.join(output_path,'UMAP_notIntegrated.pdf'),transparent=True,dpi=1000)

[2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:53] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:54] findfont: Font family 'FreeSans' not found.

[2024-04-30 09:03:55] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:55] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:55] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:55] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:55] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:57] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:03:58] findfont: Font family 'FreeSans' not found.

###UMAP after sample integration
###Add deconvolution values stored in 'obsm'['qc_m']
adata_integrate.obs[gene_sig.columns]=pd.DataFrame(adata_integrate.obsm['qc_m'],
                                                   columns=gene_sig.columns,
                                                   index=adata_integrate.obs_names)
sc.pp.neighbors(adata_integrate,use_rep='qc_m',n_neighbors=20)
sc.tl.umap(adata_integrate,  min_dist=0.2)

#Plot
fig, ax = plt.subplots(1, 1, figsize=(10,10), dpi=300)
ax = sc.pl.umap(adata_integrate,color='anonymized_id',
                frameon=False, s=5, ax=ax,
                title='UMAP after Starfysh sample integration'
                )
fig.savefig(os.path.join(output_path,'UMAP_Integrated.pdf'),transparent=True,dpi=1000)

[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:34] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:35] findfont: Font family 'FreeSans' not found.

[2024-04-30 09:09:36] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:36] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:36] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:36] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:36] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:38] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:39] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:39] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:39] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:39] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:39] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:39] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:09:39] findfont: Font family 'FreeSans' not found.

####UMAP plotting some pops of interest....
#For Treg
sc.settings.set_figure_params(dpi=300, facecolor='white')
sc.settings.set_figure_params(dpi=500, facecolor='white')
fig,ax = plt.subplots(1,1,figsize=(4,3.2),dpi=500)

sc.pl.umap(adata_integrate,color="Treg",frameon=False,
           vmax=0.2,
           s=10,
           cmap='Spectral_r',
           ax=ax,
           title=''
          )
fig.savefig(os.path.join(output_path,'UMAP_Integrated_Treg.pdf'),transparent=True,dpi=1000,bbox_inches='tight')

[2024-04-30 09:11:30] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:30] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:30] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:30] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:30] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:30] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:30] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:30] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found.

[2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:31] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:32] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:32] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:32] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:32] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:32] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:32] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:33] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:33] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:33] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:33] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:33] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:33] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:33] findfont: Font family 'FreeSans' not found.
[2024-04-30 09:11:33] findfont: Font family 'FreeSans' not found.